unWantedComp              package:ScISI              R Documentation

_A _f_u_n_c_t_i_o_n _t_o _m_a_n_u_a_l_l_y _r_e_m_o_v_e _p_r_o_t_e_i_n _c_o_m_p_l_e_x_e_s _f_r_o_m _s_o_m_e _i_n
_s_i_l_i_c_o _i_n_t_e_r_a_c_t_o_m_e

_D_e_s_c_r_i_p_t_i_o_n:

     This function takes in an in silico interactome by its bipartite
     graph representation and a character vector of complex ID's. The
     function parses through the column names of the in silico
     interactome and removes those columns whose names are found in the
     character vector.

_U_s_a_g_e:

     unWantedComp(ISI, unwantedComplex = c("GO:0000262", "GO:0000228",
     "GO:0000775", "GO:0010008", "GO:0005792", "GO:0005768", "GO:0005769",
     "GO:0005770", "GO:0005777", "GO:0005844", "GO:0001400"), unwantedGenes =
     c("RNA_TLC1", "SNRNA_NME1","RNA_RNASE-P"))

_A_r_g_u_m_e_n_t_s:

     ISI: The in silico interactome as a bipartite graph

unwantedComplex: A character vector. Each entry is a protein complex id
          for which should be removed from the interactome.

unwantedGenes: A character vector of gene names that will be deleted
          from the row indexing set of the in silico interactome.

_V_a_l_u_e:

     An incidence matrix. A new matrix with those columns indexed by
     unwantedComplex removed. It will also remove any protein which is
     now no longer contained in any protein complex.

_N_o_t_e:

     The entries of unwantedComplex must be found in the column names
     of ISI, otherwise, they will not be removed. This is especially
     important since there are many id's that index the same protein
     complex.

_A_u_t_h_o_r(_s):

     T. Chiang

_E_x_a_m_p_l_e_s:

     #mips = getMipsInfo()
     #go = getGOInfo()
     #mipsM = createMipsMatrix(mips)
     #goM = createGOMatrix(go)
     #mips2go = runCompareComplex(mipsM, goM, byWhich = "ROW")
     #merged = mergeBGMat(mipsM, goM, mips2go$toBeRm)
     #ISI = unWantedComp(merged)

